Homologous recombination with linear DNA for deletion of the original selleck target gene was performed according to the procedure previously reported with modifications (Datsenko & Wanner, 2000). In brief, PCR products containing the kan gene from pKD4 or pKD13 were electroporated into the E. coli strain harboring pKD46r and grown in LB agar containing KM (either 5 or 25 μg mL−1) and/or 3-β-indoleacrylic acid (IAA, inhibitor of TrpR) (25 μg mL−1). Deletion of the target gene was examined by PCR. Colonies grown in LB agar containing KM (5 μg mL−1) and IAA (25 μg mL−1) were suspended with sterile saline. Suspensions were diluted 10-fold serially with sterile

saline. Then, one hundred microliters of samples was spread onto LB agar without any supplement, LB agar containing IAA (25 μg mL−1), LB agar containing tryptophan (Trp, 1 mg mL−1), or LB agar containing Trp (1 mg mL−1) plus IPTG (10 mM) and then cultured at 37 °C for > 24 h. Finally, the number of colonies grown on the plates was enumerated. Colony-forming capacity was determined selleck chemicals by the appearance of visible colonies within

48 h of cultivation, and as a positive control, approximately 1000 colony-forming units (CFU) per plate of bacteria were spread on a plate. Colonies grown on LB agar containing KM (5 μg mL−1) and IAA (25 μg mL−1) were suspended with sterile saline and adjusted to OD600 nm = 0.08–0.10. These solutions were diluted 10 000-fold in LB broth and incubated in a shaking incubator at 120 r.p.m. at 37 °C for 2 h. After

incubation, IAA (25 μg mL−1) or IPTG (10 mM) plus Trp (1 mg mL−1) was added to each tube. Aliquots from each tube were removed at −1, 0, 1, 3, and 6 h, and then 10-fold serial dilutions were spread onto LB agar plates containing KM (5 μg mL−1) and IAA (25 μg mL−1). Viable colonies were enumerated after 24–48 h incubation at 37 °C with the limit of detection for the time-kill studies being 10 CFU mL−1. When no viable colony was detected in the undiluted culture, the sample was defined as 10 CFU mL−1. The wild-type lacI promoter is Selleck Dolutegravir very weak (Calos, 1978). For efficient lacI gene expression, the lacI promoter of E. coli K-12 MG1655 was replaced with lacI-35-10 promoter (Glascock & Weickert, 1998) by homologous recombination, and then the promoter of the clpA gene was replaced with lacUV5 promoter (Lanzer & Bujard, 1988), and the ORF of HA tag was fused in-frame to 3′-end of the clpA gene ORF. Next, the ORF region of the sdaB (Shao & Newman, 1993), a homologue of sdaA that is not essential for bacterial survival, was replaced with CP25e promoter, a constitutive promoter with modification for optimal sequences for E. coli (Jensen & Hammer, 1998), and the ubp1 ORF fused in-frame with FLAG tag ORF at 3′-end. No apparent phenotypic change by deletion of sdaB was observed. The protein expression of ClpA-HA (IPTG supplemented condition) and UBP1-FLAG in this strain was confirmed by Western blotting using anti-HA and anti-FLAG antibody respectively (data not shown).